Integrated Genomics Operation (IGO) -- Core Facility

Agnès Viale (Core Facility Head)
E-mail(s)
vialea@mskcc.org

The Integrated Genomics Operation (IGO) at Memorial Sloan Kettering is a collaborative core facility focused on generating high-quality genomics data for basic, translational, or clinical research projects. The main technology platforms we use are microarray and next-generation sequencing. We offer researchers comprehensive genomics services, from pathological review of tissue samples to data generation.

Sample preparation may include pathological review, phenotypic characterization, and microdissection.  We help with the extraction of RNA and DNA from both standard and challenging sources and perform sample quality control assessment. A range of functional genomics applications are available, including gene expression analysis; array comparative genomic hybridization; microRNA, single-nucleotide polymorphism (SNP), and chromatin immunoprecipitation; and methylation analysis measured with Affymetrix, Illumina, or Agilent microarrays. Microarray validation by real-time PCR and digital PCR is also offered.

In recent years, the IGO has expanded its portfolio of measurement technologies to include a number of next- generation sequencing instruments such as the PGM and Proton sequencers from Ion Torrent and the HiSeq/MiSeq systems from Illumina. These sequencing technologies allow us to conduct high-throughput analysis of a range of genomics applications such as variant detection, epigenomics, transcriptome sequencing, and more.

In addition, the IGO evaluates new technologies to support cancer science at Memorial Sloan Kettering. Our latest acquisitions include a single molecule sequencer (MinION , Oxford Nanopore Technologies) and a C1 Single-Cell Autoprep System.

Services

The Integrated Genomics Operation offers the following RNA and DNA analysis services.

RNA Analysis

  • RNA extraction from fresh frozen or FFPE tissue, cells, or other sources such as blood, saliva, buccal swab, and cytospin
  • RNA quality control and quantification on the Agilent Bioanalyzer
  • Transcriptome analysis or discovery using Affymetrix arrays, RNAseq (Proton, Hiseq), and digital and real-time PCR
  • Targeted gene expression analysis using Nanostring or digital PCR

DNA Analysis

  • Review and microdissection of tissue from slides
  • Sectioning of fresh frozen and FFPE tissues
  • H&E staining
  • DNA extraction from fresh frozen or FFPE tissue, cells, or other sources such as blood, saliva, buccal swab, and cytospin
  • Detection of SNPs and somatic mutations using Affymetrix SNP6 arrays, Sequenom, whole exome sequencing, targeted resequencing (nimblegen or Ampliseq custom panel, IMPACT), and whole genome sequencing at the New York Genome Center
  • Sanger sequencing
Publications